From ce23b7810e0a9fea03e3f46a14319e1012d4eabf Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:41:43 +0000
Subject: [PATCH] Reading features files readded as ref to FeatureRenderer is
 required

---
 src/jalview/gui/AlignFrame.java |  113 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 99 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5685e42..de2d3d1 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -770,6 +770,8 @@ public class AlignFrame
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
+        System.out.println("Exception whilst pasting: "+ex);
         // could be anything being pasted in here
     }
 
@@ -1123,6 +1125,8 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)
      alignPanel.overviewPanel.updateOverviewImage();
 
+   viewport.alignment.adjustSequenceAnnotations();
+
    alignPanel.repaint();
  }
 
@@ -2533,17 +2537,73 @@ public void showTranslation_actionPerformed(ActionEvent e)
  */
 public boolean parseGroupsFile(String file)
 {
-  AnnotationReader ar = new AnnotationReader();
+    try
+    {
+      BufferedReader in = new BufferedReader(new FileReader(file));
+      SequenceI seq = null;
+      String line, type, desc, token;
+
+      int index, start, end;
+      StringTokenizer st;
+      SequenceFeature sf;
+      int lineNo = 0;
+      while ( (line = in.readLine()) != null)
+      {
+        lineNo++;
+        st = new StringTokenizer(line, "\t");
+        if (st.countTokens() == 2)
+        {
+          type = st.nextToken();
+          UserColourScheme ucs = new UserColourScheme(st.nextToken());
+          alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          continue;
+        }
+
+        while (st.hasMoreElements())
+        {
+          desc = st.nextToken();
+          token = st.nextToken();
+          if (!token.equals("ID_NOT_SPECIFIED"))
+          {
+            index = viewport.alignment.findIndex(viewport.alignment.findName(token));
+            st.nextToken();
+          }
+          else
+          {
+            index = Integer.parseInt(st.nextToken());
+          }
+
+          start = Integer.parseInt(st.nextToken());
+          end = Integer.parseInt(st.nextToken());
+
+          seq = viewport.alignment.getSequenceAt(index);
+          start = seq.findIndex(start) - 1;
+          end = seq.findIndex(end) - 1;
+
+          type = st.nextToken();
+
+          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
+          }
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+
+          seq.getDatasetSequence().addSequenceFeature(sf);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing groups file: " + ex);
+      return false;
+    }
 
-  if (ar.readGroupsFile(alignPanel.seqPanel.seqCanvas.getFeatureRenderer(),
-                        viewport.alignment, file))
-  {
     viewport.showSequenceFeatures = true;
     alignPanel.repaint();
     return true;
-  }
-  else
-    return false;
 }
 
 public void dragEnter(DropTargetDragEvent evt)
@@ -2603,23 +2663,48 @@ public void drop(DropTargetDropEvent evt)
 
     if (files != null)
     {
-      AnnotationReader ar = new AnnotationReader();
       try
       {
+        boolean isAnnotation = false;
+
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
-          if(! ar.readAnnotationFile(viewport.alignment, file) )
-            parseGroupsFile(file);
-          else
+
+          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
+
+          if( !isAnnotation )
           {
+            boolean isGroupsFile = parseGroupsFile(file);
+            if (!isGroupsFile)
+            {
+              String protocol = "File";
+              String format = jalview.io.IdentifyFile.Identify(file, protocol);
+              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
 
+              FastaFile ff = new FastaFile();
+              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+              c.setContents(new StringSelection(ff.print(sequences)), this);
+
+              this.paste(false);
+
+            }
           }
         }
 
-        alignPanel.annotationPanel.adjustPanelHeight();
-        alignPanel.annotationScroller.validate();
-        alignPanel.repaint();
+        if(isAnnotation)
+        {
+          int height = alignPanel.annotationPanel.adjustPanelHeight();
+          alignPanel.annotationScroller.setPreferredSize(
+              new Dimension(alignPanel.annotationScroller.getWidth(),
+                            height));
+
+          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+              alignPanel.annotationSpaceFillerHolder.getWidth(),
+              height));
+
+          alignPanel.addNotify();
+        }
       }
       catch (Exception ex)
       {
-- 
1.7.10.2